Corset: Enabling differential gene expression analysis for de novo assembled transcriptomes
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2014-07-26
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Genome Biology
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BMC
Melbourne Authors
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School of BioSciences
School of Physics
School of Physics
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Journal Article
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Davidson, N. M. & Oshlack, A. (2014). Corset: Enabling differential gene expression analysis for de novo assembled transcriptomes. Genome Biology, 15 (7), https://doi.org/10.1186/s13059-014-0410-6.
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Abstract
Next generation sequencing has made it possible to perform differential gene expression studies in non-model organisms. For these studies, the need for a reference genome is circumvented by performing de novo assembly on the RNA-seq data. However, transcriptome assembly produces a multitude of contigs, which must be clustered into genes prior to differential gene expression detection. Here we present Corset, a method that hierarchically clusters contigs using shared reads and expression, then summarizes read counts to clusters, ready for statistical testing. Using a range of metrics, we demonstrate that Corset out-performs alternative methods. Corset is available from https://code.google.com/p/corset-project/.